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Activate multiqc ai summaries #1495

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wants to merge 17 commits into from
Closed

Activate multiqc ai summaries #1495

wants to merge 17 commits into from

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pinin4fjords
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@pinin4fjords
feat: add MultiQC AI summaries support
efd25a2 
Add support for MultiQC's AI-powered summaries feature via new parameter: - Add enable_multiqc_ai boolean parameter to schema - Add --ai flag to MultiQC args when enabled - Use nf-core standard array syntax for MultiQC args
@pinin4fjords
feat: Add MultiQC AI summary options with type selection
41b2187
@pinin4fjords
feat: Add Seqera access token configuration for MultiQC AI
fade208
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jan 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ae15852

+| ✅ 190 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-28 15:47:56

@pinin4fjords
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Needs nf-core/modules#7364

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@nf-core-bot fix linting

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@nf-core-bot fix linting

maxulysse
maxulysse approved these changes Jan 27, 2025
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<3

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Report from test profile: multiqc_report rnaseq_test.html.zip

adamrtalbot
adamrtalbot reviewed Jan 28, 2025
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nextflow.config
Comment on lines +300 to +304
// Propagate API keys to MultiQC
System.getenv('SEQERA_ACCESS_TOKEN')?.with { SEQERA_ACCESS_TOKEN = it }
System.getenv('TOWER_ACCESS_TOKEN')?.with { TOWER_ACCESS_TOKEN = it }
System.getenv('OPENAI_API_KEY')?.with { OPENAI_API_KEY = it }
System.getenv('ANTHROPIC_API_KEY')?.with { ANTHROPIC_API_KEY = it }
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I know nf-core wants to be 'batteries included', but this does feel like a lot of stuff when it's user configurable.

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I quite like the approach, but I'm not sure that it'll be allowed with the new config parser :/

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But I don't want to be the user that configures it ;-)

@pinin4fjords pinin4fjords marked this pull request as draft January 29, 2025 09:03
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Converted to draft pending conclusion of community discussions as to how good an idea this is

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pinin4fjords commented Jan 29, 2025 •
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Closing for now after discussion, we'll wait and see how people end up using this. Once we update the multiqc module you will already be able to use this functionality by following the MultiQC docs.

If you come across this wanting to use the functionality, you'll need custom configuration like:

env{
    // Propagate API keys to MultiQC
    System.getenv('MULTIQC_AI')?.with { MULTIQC_AI = it }
    System.getenv('OPENAI_API_KEY')?.with { OPENAI_API_KEY = it }
}

... and then run the workflow like this:

export OPENAI_API_KEY=xxx
export MULTIQC_AI=1
nextflow run nf-core/rnaseq

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@adamrtalbot adamrtalbot adamrtalbot left review comments

@ewels ewels ewels left review comments

@maxulysse maxulysse maxulysse approved these changes

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@pinin4fjords @nf-core-bot @ewels @maxulysse @adamrtalbot